Re: [Psidev-ms-dev] binaryArrayData lengths

[Matthew C. <mat...@va...>]

I can live with that (or "length" or "peakCount").

-Matt


Eric Deutsch wrote:
> So there seems to be broad consensus (4 for 4;) that moving the
> arrayLength up a little higher is a good idea.  So instead of:
>
> <spectrum id="S19" scanNumber="19" msLevel="1">
> 	<spectrumDescription>
> 		...
> 	</spectrumDescription>
> 	<binaryDataArray arrayLength="1313" encodedLength="5433"
> dataProcessingRef="Xcalibur Processing">
> 		...
> 		<binary>AAAAwDsGeUAAAAD...</binary>
> 	</binaryDataArray>
> 	<binaryDataArray arrayLength="1313" encodedLength="4892">
> 		...
> 		<binary>AAAAAIBJxk...</binary>
> 	</binaryDataArray>
> </spectrum>
>
> We will have:                                  !!!!!!!!!!!!!!!!!!
>
> <spectrum id="S19" scanNumber="19" msLevel="1" arrayLength="1313">
> 	<spectrumDescription>
> 		...
> 	</spectrumDescription>
> 	<binaryDataArray encodedLength="5433"
> dataProcessingRef="Xcalibur Processing">
> 		...
> 		<binary>AAAAwDsGeUAAAAD...</binary>
> 	</binaryDataArray>
> 	<binaryDataArray encodedLength="4892">
> 		...
> 		<binary>AAAAAIBJxk...</binary>
> 	</binaryDataArray>
> </spectrum>
>
>
> Agreed?
>
>
>
>   
>> -----Original Message-----
>> From: psi...@li...
>>     
> [mailto:psidev-ms-dev-
>   
>> bo...@li...] On Behalf Of Matthew Chambers
>> Sent: Wednesday, February 06, 2008 10:49 AM
>> To: Mass spectrometry standard development
>> Subject: Re: [Psidev-ms-dev] binaryArrayData lengths
>>
>> I agree that the primary data arrays should probably be treated as
>> special in the schema so it's clear that they are paired values and
>>     
> thus
>   
>> peak count could move into the spectrum element or
>>     
> spectrumDescription.
>   
>> There should still be options to have additional arrays that aren't
>>     
> the
>   
>> same as the main arrays (for example, an additional set of arrays, one
>> for a subset of the m/zs and the other for peak charge information).
>>
>> -Matt
>>
>>
>> Kessner, Darren E. wrote:
>>     
>>> Any other comments regarding <binaryArrayData> lengths?
>>>
>>>
>>>       
>>>> (from Rune)
>>>> If they have to be equal size, then
>>>> that size ought to be specified in the spectrumDescription.
>>>>
>>>>         
>>> I agree -- I would like to encode the length in <spectrum> somewhere
>>> (either attribute or cvParam) so that:
>>> 1) it's clear that the arrays are of equal size
>>> 2) Readers don't have to peek into the attributes of the first
>>> <binaryArrayData> to get the info
>>>
>>> I need this right now for the MSData RAMP adapter code, so I'll
>>>       
> encode
>   
>>> it as a <userParam> until a decision has been made on the
>>>       
> specification.
>   
>>> Darren
>>>       
>>
>>     
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